| stringDist {Biostrings} | R Documentation |
Computes the Levenshtein edit distance or pairwise alignment score matrix for a set of strings.
stringDist(x, method = "levenshtein", ignoreCase = FALSE, diag = FALSE, upper = FALSE, ...)
## S4 method for signature 'XStringSet':
stringDist(x, method = "levenshtein", ignoreCase = FALSE, diag = FALSE,
upper = FALSE, type = "global", quality = PhredQuality(22L),
substitutionMatrix = NULL, fuzzyMatrix = NULL, gapOpening = 0,
gapExtension = -1)
## S4 method for signature 'QualityScaledXStringSet':
stringDist(x, method = "quality", ignoreCase = FALSE,
diag = FALSE, upper = FALSE, type = "global", substitutionMatrix = NULL,
fuzzyMatrix = NULL, gapOpening = 0, gapExtension = -1)
x |
a character vector or an XStringSet object. |
method |
calculation method. One of "levenshtein",
"quality", or "substitutionMatrix". |
ignoreCase |
logical value indicating whether to ignore case during scoring. |
diag |
logical value indicating whether the diagonal of the matrix
should be printed by print.dist. |
upper |
logical value indicating whether the diagonal of the matrix
should be printed by print.dist. |
type |
(applicable when method = "quality" or
method = "substitutionMatrix").
type of alignment. One of "global", "local", and
"overlap", where
"global" = align whole strings with end gap penalties,
"local" = align string fragments,
"overlap" = align whole strings without end gap penalties. |
quality |
(applicable when method = "quality").
object of class XStringQuality representing the quality scores
for x that are used in a quality-based method for generating a
substitution matrix. |
substitutionMatrix |
(applicable when
method = "substitutionMatrix").
symmetric matrix representing the fixed substitution scores in the
alignment. |
fuzzyMatrix |
(applicable when method = "quality").
fuzzy match matrix for quality-based alignments. It takes values between 0
and 1; where 0 is an unambiguous mismatch, 1 is an unambiguous match, and
values in between represent a fraction of "matchiness". |
gapOpening |
(applicable when method = "quality" or
method = "substitutionMatrix").
penalty for opening a gap in the alignment. |
gapExtension |
(applicable when method = "quality" or
method = "substitutionMatrix").
penalty for extending a gap in the alignment |
... |
optional arguments to generic function to support additional methods. |
Uses the underlying pairwiseAlignment code to compute the distance/alignment score matrix.
Returns an object of class "dist".
P. Aboyoun
dist, agrep, pairwiseAlignment, substitution.matrices
stringDist(c("lazy", "HaZy", "crAzY"))
stringDist(c("lazy", "HaZy", "crAzY"), ignoreCase = TRUE)
data(phiX174Phage)
plot(hclust(stringDist(phiX174Phage), method = "single"))
data(srPhiX174)
stringDist(srPhiX174[1:4])
stringDist(srPhiX174[1:4], method = "quality",
quality = SolexaQuality(quPhiX174[1:4]),
gapOpening = -10, gapExtension = -4)